CFTR gene mutation in patients with apparently idiopathic pancreatitis: lack of phenotype-genotype correlation

Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test?

PURPOSE

To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied.

METHODS

In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied.

RESULTS

The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests.

CONCLUSION

Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.

Frequency of allele variations in the CFTR gene in a Mexican population

Background

Cystic fibrosis (CF) is an autosomal recessive disorder caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CF variants incidence is highly variable and even undetermined in some countries like Mexico.

Methods

In this study, the allele frequencies of 361 variants in the CFTR gene were investigated in 1455 Mexicans without a CF or CFTR-related disorders (CFTR-RD) diagnosis. We also performed a statistical comparative analysis against allele frequencies of different populations to measure genetic differences in the prevalence of CFTR variants.

Results

In the vast majority of cases, the allele frequencies of this cohort were comparable to those found in other populations. However, some variants displayed significant differences in their allele frequencies when compared with European and African populations.

Conclusions

This study provides information about CFTR variants to predict the prevalence of CF in Mexico and uncover other unknown but frequent pathogenic variants in the country. Additionally, other CFTR-RD variants have also been studied using population data of the same CFTR variants. Studies like this could help develop a regional molecular diagnostic screen to optimize the medical care of CF patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-021-01111-w.

A high prevalence of genetic polymorphisms in idiopathic and alcohol-associated chronic pancreatitis patients in Ireland

BACKGROUND

Individual genetic architecture is considered central to susceptibility and progression of disease in chronic pancreatitis. The study aimed to evaluate the presence of common pancreatic gene mutations in a defined cohort of idiopathic and alcohol-induced chronic pancreatitis patients in Ireland.

METHODS

The study comprised patients with idiopathic and alcohol-induced chronic pancreatitis and historic controls. Variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, cationic trypsinogen (PRSS1) gene and serine protease inhibitor kazal type-1 (SPINK1) gene, were assessed by Taqman© genotyping assay.

RESULTS

Of n = 126 patients and n = 167 controls, mutations were detected in 23 (20%) and in 10 (6%) respectively (P < 0.001). The majority of mutations found were in the SPINK1 gene variant N34S (13%) which increased disease risk almost six-fold (OR 5.9). Neither CFTR severe mutation (F508del) (P = 0.649) nor mild variant (R117H) (P = 0.327) were over-represented amongst patients compared to control subjects. PRSS1 variants were not detected in either patient or control subjects.

CONCLUSION

There was a significant prevalence of chronic pancreatitis-associated gene mutations in this well-phenotyped cohort. In patients with alcohol-related or idiopathic chronic pancreatitis, the possibility of genetic mutations in the SPINK 1 gene should be considered as a contributing aetiology factor.

Carriers of cystic fibrosis among sperm donors: complete CFTR gene analysis versus CFTR genotyping

OBJECTIVE

To determine the frequency of cystic fibrosis (CF) carriers among sperm donors in Spain studied through a complete analysis of the CFTR gene and to compare the results with those that would have been obtained by the 4 genotyping panels of the CFTR gene most commonly used as a carrier test in the context of assisted reproduction in our country.

DESIGN

Descriptive observational study.

SETTING

Private center.

PATIENTS

Nine hundred thirty-five sperm donors, from January 2014 to June 2019.

INTERVENTION

None.

MAIN OUTCOME MEASURE

Presence of pathogenic variants in the CFTR gene.

RESULTS

17% of the donors were carriers of at least 1 pathogenic variant in CFTR, with 39 different pathogenic variants detected. Only 4 of these 39 variants (10.27%) would have been detected by the 4 genotyping tests considered, and 22 variants (56.41%) would not have been detected by any of the genotyping tests. The pathogenic variants of the CFTR gene included in the different genotyping tests analyzed vary widely, and <50% are common to all of them.

CONCLUSIONS

Although the was not based in the general population, these results show that the use of genotyping tests is associated with a high reproductive risk, because the rate of detection of CF carriers was lower when these panels were applied, in comparison with the complete study of the CFTR gene. We recommend that complete sequencing of the CFTR gene by next-generation sequencing be performed as a screening method for CF in sperm donors.

Benign and Deleterious Cystic Fibrosis Transmembrane Conductance Regulator Mutations Identified by Sequencing in Positive Cystic Fibrosis Newborn Screen Children from California

Background

Of the 2007 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutations, 202 have been assigned disease liability. California’s racially diverse population, along with CFTR sequencing as part of newborn screening model, provides the opportunity to examine the phenotypes of children with uncategorized mutations to help inform disease liability and penetrance.

Methods

We conducted a retrospective cohort study based on children screened from 2007 to 2011 and followed for two to six years. Newborns that screened positive were divided into three genotype groups: those with two CF-causing mutations (CF-C); those with one mutation of varying clinic consequence (VCC); and those with one mutation of unknown disease liability (Unknown). Sweat chloride tests, pancreatic sufficiency status, and Pseudomonas aeruginosa colonization were compared.

Results

Children with two CF-causing mutations had a classical CF phenotype, while 5% of VCC (4/78) and 11% of Unknown (27/244) met diagnostic criteria of CF. Children carrying Unknown mutations 2215insG with D836Y, and T1036N had early and classical CF phenotype, while others carrying 1525-42G>A, L320V, L967S, R170H, and 296+28A>G had a benign clinical presentation, suggesting that these are non-CF causing.

Conclusions

While most infants with VCC and Unknown CFTR mutations do not meet diagnostic criteria for CF, a small proportion do. These findings highlight the range of genotypes and phenotypes in the first few years of life following CF newborn screening when CFTR sequencing is performed.

Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis

CFTR is a dynamically regulated anion channel. Intracellular WNK1-SPAK activation causes CFTR to change permeability and conductance characteristics from a chloride-preferring to bicarbonate-preferring channel through unknown mechanisms. Two severe CFTR mutations (CFTRsev) cause complete loss of CFTR function and result in cystic fibrosis (CF), a severe genetic disorder affecting sweat glands, nasal sinuses, lungs, pancreas, liver, intestines, and male reproductive system. We hypothesize that those CFTR mutations that disrupt the WNK1-SPAK activation mechanisms cause a selective, bicarbonate defect in channel function (CFTRBD) affecting organs that utilize CFTR for bicarbonate secretion (e.g. the pancreas, nasal sinus, vas deferens) but do not cause typical CF. To understand the structural and functional requirements of the CFTR bicarbonate-preferring channel, we (a) screened 984 well-phenotyped pancreatitis cases for candidate CFTRBD mutations from among 81 previously described CFTR variants; (b) conducted electrophysiology studies on clones of variants found in pancreatitis but not CF; (c) computationally constructed a new, complete structural model of CFTR for molecular dynamics simulation of wild-type and mutant variants; and (d) tested the newly defined CFTRBD variants for disease in non-pancreas organs utilizing CFTR for bicarbonate secretion. Nine variants (CFTR R74Q, R75Q, R117H, R170H, L967S, L997F, D1152H, S1235R, and D1270N) not associated with typical CF were associated with pancreatitis (OR 1.5, p = 0.002). Clones expressed in HEK 293T cells had normal chloride but not bicarbonate permeability and conductance with WNK1-SPAK activation. Molecular dynamics simulations suggest physical restriction of the CFTR channel and altered dynamic channel regulation. Comparing pancreatitis patients and controls, CFTRBD increased risk for rhinosinusitis (OR 2.3, p<0.005) and male infertility (OR 395, p<<0.0001). WNK1-SPAK pathway-activated increases in CFTR bicarbonate permeability are altered by CFTRBD variants through multiple mechanisms. CFTRBD variants are associated with clinically significant disorders of the pancreas, sinuses, and male reproductive system.

Pancreatic exocrine function and morphology following an episode of acute pancreatitis

OBJECTIVE

The objective of this study was to assess pancreatic exocrine function (PEF) and morphology in patients recovering from a first episode of acute pancreatitis (AP).

METHODS

Sixty-five eligible patients recovering from AP and 70 healthy volunteers were enrolled in this study. We evaluated PEF by fecal elastase 1 (FE-1) and used ultrasonography to detect pancreatic morphology for all patients and 40 controls.

RESULTS

Exocrine pancreatic insufficiency (EPI) incidence in the severe and mild AP subgroups was 60.5% and 39.5%, respectively. The FE-1 level in patients who had undergone surgical care was significantly lower compared with the controls (P < 0.01), whereas no difference was observed between the alcoholic and nonalcoholic groups (P > 0.05). Surprisingly, the defecation change correlated with the EPI level. In these patients, a stepwise recovery was observed over the following 2.4 years. Compared with the controls, the diameter of pancreatic duct was enlarged, and abdominal pain during recovery was found to be the independent risk factor for pancreatic duct expansion, although a significant difference was not exhibited between the AP subgroups concerning FE-1 concentration (P = 0.591).

CONCLUSIONS

Our results indicated that many AP patients may have long-lasting EPI and an expanded main pancreatic duct; thus, routine evaluation of PEF is warranted.

Pancreas divisum is not a cause of pancreatitis by itself but acts as a partner of genetic mutations

OBJECTIVES

The role of pancreas divisum (PD) as a cause of acute recurrent or chronic pancreatitis (AR/CP) is still a matter of debate.

METHODS

The aims of this study were to evaluate the frequency of PD diagnosed using magnetic resonance cholangiopancreatography (MRCP) in patients with AR/CP of unknown origin (n=40) after careful exclusion of all known causes and to test the hypothesis of an interaction between anatomical (PD) and functional genetic anomalies (SPINK1, PRSS1, or CFTR gene mutations or polymorphisms (n=19, 25, and 30, respectively)) that could result in AR/CP. Patients with alcohol-induced pancreatitis (n=29) and subjects who had MRCP for a nonpancreatic disease (n=45) served as controls.

RESULTS

PD frequency was 7% in subjects without pancreatic disease, 7% in patients with alcohol-induced pancreatitis, and 5, 16, 16, and 47% in those with idiopathic, and PRSS1-, SPINK1-, and CFTR-associated pancreatitis, respectively (P<0.0001). There was no significant difference between idiopathic pancreatitis and the two control groups. The frequency of PD was higher in patients with CFTR gene-associated pancreatitis as compared with those with idiopathic and alcoholic pancreatitis (P<0.0001) and with those with SPINK1 and PRSS1 gene-associated pancreatitis (P<0.02).

CONCLUSIONS

The frequency of PD was not different in patients with idiopathic pancreatitis as compared with controls, demonstrating that PD by itself is not a cause of pancreatitis. PD frequency was higher in patients with genetic pancreatitis, especially in those with CFTR mutations or polymorphisms, suggesting a cumulative effect of these two cofactors.

Etiology and diagnosis of acute biliary pancreatitis

Establishing a biliary etiology in acute pancreatitis is clinically important because of the potential need for invasive treatment, such as endoscopic retrograde cholangiopancreatography. The etiology of acute biliary pancreatitis (ABP) is multifactorial and complex. Passage of small gallbladder stones or biliary sludge through the ampulla of Vater seems to be important in the pathogenesis of ABP. Other factors, such as anatomical variations associated with an increased biliopancreatic reflux, bile and pancreatic juice exclusion from the duodenum, and genetic factors might contribute to the development of ABP. A diagnosis of a biliary etiology in acute pancreatitis is supported by both laboratory and imaging investigations. An increased serum level of alanine aminotransferase (>1.0 microkat/l) is associated with a high probability of gallstone pancreatitis (positive predictive value 80-90%). Confirmation of choledocholithiasis is most accurately obtained using endoscopic ultrasonography or magnetic resonance cholangiopancreatography. This Review discusses the pathogenesis of ABP and the clinical techniques used to predict and establish a biliary origin in patients with suspected ABP.